db <- dbConnect(SQLite(), dbname="../COVIDDB/CORVID.sqlite3")
US <- dbGetQuery(db, "SELECT * FROM JHUDATA
WHERE country ='US'")
US$date <- as.Date(US$date)
US <- US%>% mutate(daily_deaths = deaths - lag(deaths))
US <- US%>% mutate(daily_cases = confirmed - lag(confirmed))
US <- US%>% mutate(daily_recovery = recovered - lag(recovered))
US Recoveries by Date (Daily and Accumliated)
plot1 <- US %>% ggplot() + geom_line(aes(x=date,y=recovered),col="blue",lwd=1) +
labs(title="US Accumliated Recoveries to Date",
capton="(Source: https://coronavirus.jhu.edu/map.html")
ggplotly(plot1)
plot2 <- US %>% ggplot() + geom_line(aes(x=date,y=daily_recovery),col="blue",lwd=1) +
labs(title="US Daily Recoveries by Date",
caption="(https://coronavirus.jhu.edu/map.html)")
ggplotly(plot2)
Comparing Daily Cases to Recoveries
US %>% ggplot() + geom_line(aes(x=date,y=daily_recovery,col="Recoveries"),lwd=1) +
labs(title="US Daily Cases and Recoveries by Date",
caption="(Source: https://coronavirus.jhu.edu/map.html)",
y="Daily Cases and Recoveries",subtitle="Apr. 25, 2020") +
geom_line(aes(x=date,y=daily_cases,col="Cases"),lwd=1) +
easy_remove_x_axis()
## Warning: Removed 1 row(s) containing missing values (geom_path).
## Warning: Removed 1 row(s) containing missing values (geom_path).

US %>% ggplot() + geom_line(aes(x=date,y=daily_recovery,col="Recoveries"),lwd=1) +
labs(title="US Daily Cases and Recoveries by Date",
caption="(Source: https://coronavirus.jhu.edu/map.html)",
y="Log of Daily Cases and Recoveries",subtitle="Apr. 25,2020") +
geom_line(aes(x=date,y=daily_cases,col="Cases"),lwd=1) +
scale_y_log10()
## Warning in self$trans$transform(x): NaNs produced
## Warning: Transformation introduced infinite values in continuous y-axis
## Warning: Transformation introduced infinite values in continuous y-axis
## Warning: Removed 1 row(s) containing missing values (geom_path).
## Warning: Removed 1 row(s) containing missing values (geom_path).

US %>% ggplot() +
geom_line(aes(x=date,y=daily_recovery,col="Recoveries"),lwd=1) +
labs(title="US Daily Cases and Recoveries by Date" ,
y="Daily Cases and Recoveries",subtitle="Apr. 25, 2020") +
geom_line(aes(x=date,y=daily_cases,col="Cases"),lwd=1) +
easy_remove_x_axis()
## Warning: Removed 1 row(s) containing missing values (geom_path).
## Warning: Removed 1 row(s) containing missing values (geom_path).

US %>% ggplot() + geom_line(aes(x=date,y=daily_recovery,col="Recoveries"),lwd=1) +
labs(title="US Daily Cases and Recoveries by Date",
caption="(Source: https://coronavirus.jhu.edu/map.html)",
y="Log of Daily Cases and Recoveries") +
geom_line(aes(x=date,y=daily_cases,col="Cases"),lwd=1) +
scale_y_log10()
## Warning in self$trans$transform(x): NaNs produced
## Warning: Transformation introduced infinite values in continuous y-axis
## Warning: Transformation introduced infinite values in continuous y-axis
## Warning: Removed 1 row(s) containing missing values (geom_path).
## Warning: Removed 1 row(s) containing missing values (geom_path).

Flatting the Curve
US %>% ggplot() + geom_line(aes(x=date,y=daily_deaths),col="blue",lwd=1) +
labs(title="US Deaths by Date",
y="Log10 Scale",
caption="(https://coronavirus.jhu.edu/map.html)") +
scale_y_log10()
## Warning: Transformation introduced infinite values in continuous y-axis
## Warning: Removed 1 row(s) containing missing values (geom_path).

US %>% ggplot() + geom_line(aes(x=date,y=daily_cases),col="blue",lwd=1) +
labs(title="US Cases by Date",
y="Log10 Scale",
caption="(https://coronavirus.jhu.edu/map.html)") +
scale_y_log10()
## Warning: Transformation introduced infinite values in continuous y-axis
## Warning: Removed 1 row(s) containing missing values (geom_path).

US %>% ggplot() + geom_line(aes(x=date,y=daily_recovery),col="blue",lwd=1) +
labs(title="US Recoveries by Date",
y="Log10 Scale",
caption="(https://coronavirus.jhu.edu/map.html)") +
scale_y_log10()
## Warning in self$trans$transform(x): NaNs produced
## Warning: Transformation introduced infinite values in continuous y-axis
## Warning: Removed 1 row(s) containing missing values (geom_path).

European CDC Daily Cases and Deaths
ECDC <- dbGetQuery(db, "SELECT * FROM ECDC
WHERE Countries ='USA'")
ECDC$Reported <- as.Date(ECDC$Reported)
ECDC %>% ggplot() + geom_line(aes(x=Reported,y=Cases),col="Red",lwd=1) +
labs(title="US Cases by Date",
y="Log10 of Cases",
caption="(Source: European CDc)") +
scale_y_log10()
## Warning: Transformation introduced infinite values in continuous y-axis

ECDC %>% ggplot() + geom_line(aes(x=Reported,y=Deaths),col="Red",lwd=1) +
labs(title="US Deaths by Date",
y="Log10 Scale",
caption="(Source: European CDC)") +
scale_y_log10()
## Warning: Transformation introduced infinite values in continuous y-axis
